import os
import anndata
import sys
import numpy as np
wd = '/home/clarice/Documents/SingleCell_PseudoTime/'
os.chdir(wd)
sys.path.append('extras/Stabilized_ICA')
#-- Read data
sc200 = anndata.read_h5ad('data/sc200CL_pp.h5ad')
ref_cell_line = 'JHU011_UPPER_AERODIGESTIVE_TRACT'
Preprocessing¶
import scycle as cc
cc.pp.prep_pooling(sc200)
On this warning: Nothing I can do about it as of now, it's an internal error from anndata
cc.pp.score_cell_cycle(sc200)
Integration¶
Here we run the first steps of the pipeline on the reference:
scref = sc200[sc200.obs['Cell_line'] == ref_cell_line]
cc.tl.dimensionality_reduction(scref, method = 'ica', n_comps = 30, seed = 0)
cc.tl.enrich_components(scref)
And here comes the OT integration implemented by Aziz:
cc.tl.integration(sc200, scref)
Finding the trajectory¶
cc.tl.principal_circle(sc200)
cc.pl.scatter_projection(sc200, col_var = 'Cancer_type', trajectory = True)
cc.pl.scatter_projection3d(sc200, col_var = 'Cancer_type', alpha = 0.3,
trajectory = True, size = 3, node_color = 'black', palette = 'Accent')
Find cell division moment¶
This is the clunkiest part of this pipeline, we may actually benefit from the alternative normalization based on the trajectory even if it was just to streamline this part.
cc.tl.celldiv_moment(sc200, var = 'total_counts')
cc.pl.scatter_projection(sc200, trajectory = True)
Total counts are kind of all over the place here. But there seems to be a bit of a gap around node 10?
cc.pl.scatter_projection(sc200, col_var = 'G1/S_score', trajectory = True)
cc.pl.scatter_projection(sc200, col_var = 'G2-M', trajectory = True)
cc.tl.remap_nodes(sc200, celldiv_edge = [10,11], cycle_direction = -1)
cc.tl.pseudotime(sc200)
cc.pl.hist_pseudotime(sc200)
cc.pl.scatter_cell_cycle(sc200)
cc.pl.scatter_cell_cycle(sc200, scores = 'components')
Dividing the cell cycle¶
Of note, cc.tl.cell_cycle_phase already uses the curvature settings to find the cell cycle divisions.
cc.tl.cell_cycle_phase(sc200)
cc.pl.scatter_cell_cycle(sc200, scores = 'components', alpha = 0.1)
cc.tl.annotate_cell_cycle(sc200)
cc.pl.barplot_cycle_phase(sc200)
Considering making this a piechart? I'd use our alternative plotting system with plotly for that since plotnine doesn't currently support polar coordinates, unfortunetely.
cc.pl.scatter_projection3d(sc200, col_var = 'cell_cycle_phase', size = 3)